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A New Application for Discussing Chemical Ideas

In this article, we look at a new application called Marvin Live, developed by ChemAxon for online collaboration. Marvin Live offers a novel approach to designing molecules and leading chemical discussions among remote participants.

We will describe the pharmaceutical industry and academic needs that led to these developments and the workflows made possible, all the way from simple chemical reaction drawing tasks, to connecting globally distributed research teams for project design meetings. We look at use cases that enable their use for tutoring and mentoring, and their capabilities to automate the otherwise time-consuming aspects of meeting preparations and note-taking.

Background

Commercial, as well as academic researchers have to face the problem of communication between remote participants, as discovery processes get more and more distributed1. Design and project meetings involving chemical structures in the discussions can be difficult, unless people taking part sit in the same room and use the same surface for drawing, evaluating, and discussing their ideas.

This applies not only to projects where contract research organizations or consultants are involved, but also when academic research groups, based in different universities are collaborating with each other2. In these projects sharing ideas, reflecting on problems and collecting the necessary feedback is essentially a burden.

Similarly, in the case of teaching and tutoring, ad hoc discussions between a mentor and a student can be essential, but take a high activation energy. A professor's office hours are limited; a face to face meeting is not always possible, especially with a group of students.

Over time, commonalities surfaced to how people approach this issue. In lieu of a face to face meeting, one of the most common methods is sharing data via emails either directly or to project/course specific mailing lists. This however comes with the difficulty of forming all relevant information into plain text or email attachments, and each collaborator requiring access to software that handles these attachments.

With the recent increase in availability of free video messaging solutions3, their use in scientific discussions also increased, either to share the desktop of one researcher, or to show the drawings on a whiteboard using webcams. These methods however make it very difficult for remote collaborators to actively participate, as they need to create local copies of chemical drawings, before adding an idea of their own, or storing them for reports.

Given these problems, we started to investigate if an alternative solution is possible. The requirements were to:

use digital representations of chemical structures in common file formats,

enable both data driven and discussion driven sessions, and

possess a simple and focused user interface where first time users can be just as effective as others.

Use cases

Based on qualitative feedback we identified two basic types of use in this context and developed Marvin Live to support them.

1) Usage in early phase drug discovery

In the pharmaceutical industry, this application can be used for chemical design and project discussions among collaborators in different physical locations. Individual researchers can collect and refine their ideas in non-shared rooms in advance, where they prepare and refine interesting molecules, eventually sharing them with the team. Medicinal chemists, computational chemists and biochemists can join a single virtual meeting room, to analyze, amend and make decisions about chemical ideas for a given project.

The designs during these discussions are influenced by immediate feedback on the molecules provided in the application. For this, common data sources are:

calculated physico-chemical properties and a report on how these change upon modifications,

the closest patented molecules or citations from publications,

biological data on similar or identical structures,

3D overlays on reference molecules.

A plugin system was developed to address these needs, and several plugins were developed for demonstration purposes in these categories, using ChemAxon’s property predictors, EBI’s various datasets including SureChemBL4, ChemBL5, and UniChem6; PubChem Compound7; Elsevier’s Reaxys8, eMolecules9 compound registration systems, electronic lab notebooks, and support for KNIME Server10 and Pipeline Pilot Server11. This plugin system helps researchers to analyze the chemical space they are discussing using their trusted data sources, modify the molecules to achieve the desired properties, and save important milestones for further in-silico analysis and synthesis.

Marvin Live keeps track of authorship of a chemical structure, and any attached comments and metadata used during design. At the end of each meeting, this is used to create reports that assist with further sharing of the status of the project. As various states of a design process can be retraced, the application can also be used as an idea repository for molecules.

In these cases the layout of the user interface has a medium-sized editor in the center, a list of saved or uploaded molecules on one side, and the plugins providing feedback on the other. Below the editor is a chat area for easy commenting on the structures (see fig. 1, fig. 2.).

Fig 1: Marvin Live used to mine available chemical and biological data

Fig 2: Marvin Live used to explore property space of a compound

2) Usage in academic teaching and tutoring

In the academia, Marvin Live can also be used by professors or educators and their students.

We identified typical uses for mentoring and general guidance, where students ask questions and discuss problems they face during their studies, or when writing papers. As in many cases subtle aspects of a molecule or a synthetic process are in the center of the discussion, the chemical editor has a more important role on the interface and takes up most of its area.

A slightly different scenario involving group discussions, for example students forming study groups to prepare for exams and discuss problems has also come in focus, where chat gains more importance.

To support these needs, we developed customization capabilities and an alternative user interface, that allocates more area to the chemical editor and chat, and hides options rarely relevant for these uses (see fig. 3). The application also supports tweaking the chemical editor’s toolbar and switching to presets designed for education uses.

Fig 3: Marvin Live used for tutoring in an “office hours” setting

To demonstrate these ideas and developments, we've recorded 2 simulated sessions from the point of view of a teacher. The first segment shows how a question & answer type office hour session might go, while the second segment shows practising or testing. https://youtu.be/PdDWRhvLVQg

Technology

Marvin Live is a server based application accessible through a web browser. This lets first time users immediately use the entire application, without installing any application locally. The security system supports the most common type of authentication protocols: LDAP12, Active Directory13 and SAML based single sign on14.

If the project or course benefits from database cross-checks or calculations, a JavaScript based plugin system is available to connect Marvin Live to public or custom web services. This lets administrators specify where a web service is located, what is the syntax used for queries, and how the results should be presented.

Chemical ideas can be loaded in an embedded chemical drawing application called Marvin JS15. To cover the most common research areas and teacher-student discussion topics, we made sure it supports not only the drawing of simple chemical structures, but also more advanced chemical features16, such as:

generic groups (i.e. R-groups in Markush structures) to describe collections of molecules in a compact representation

simple and complex reactions for the discussion of potential synthetic approaches

electron flow arrows for discussing reaction mechanisms

and organo-metallic compounds.

The editor also supports the calculation of the absolute stereo configuration of chiral atoms and automatic mapping of reactions. With the option to alter the general layout and switch toolbar presets, the editor can display and support complex synthetic pathways.

This editor is extended with a mechanism that in real time updates the view for everyone (see fig. 4).

Fig 4: Animated GIF of real time synchronization of chemical editors

Online tryout

Instead of a typical “Conclusions” section, we provide the following sandbox to readers of this newsletter to investigate the usefulness of this approach and experience the possibilities first hand. The sandbox is customized for the academic use cases described above.

Comments

Thank you for sharing this article on your social and semantic web enabled molecular visualization technology (I think that is an accurate statement - as does your technology not allow for the collaborative design of molecules while also using internet databases to provide information that can guide the process?) I really have a lot of questions, but will start from the most basic, which is the education-permissible use scenarios. Last night I realized you offer a free license for educators, I applied for one, and was approved this morning. So please forgive me, but I have not had time to test what I can do. Is there a specific download that you would suggest educators try, if they wanted to test your technology? Are features disabled in the educator’s edition (license)? Realize many of us have never heard of ChemAxon.

Now in one of your videos, https://youtu.be/re3LvUyCUBM , which I understand was demonstrating a research application, I saw two things that really got me thinking from an educators perspective. Two people at different locations were designing a molecule, consulting a database, and around 1:38 minutes into the video, they saved the drawing to a MS Word or PowerPoint document as a “report”. What were they saving? An image file? Or something more descriptive? Could you reopen the saved file at a later date and work on it some more? The ability of students to be able to work in groups as they explore new molecules that they design and generate reports could be built upon in many ways.

To test our technology, I think the easiest would be to grab MarvinSketch. It's a desktop chemical drawing application, with a next next next style installer, free for personal use, but the academic license you mentioned unlocks a lot of extra things in it, like medchem property predictions, a structure checker, an enumeration tool, IUPAC naming (to and from...). With the academic license, you'd have access to all capabilities, no features are disabled or limited. The chemical drawing canvas in it, is very very similar to the one used in Marvin Live. The scenarios and toolset are different however.

The report in Marvin Live takes all "saved" data from a discussion, and creates a file from it. These reports are all editable later, their goal is essentially to remove the need to manually create one after a meeting. Chemists would do that anyway, but now, a big part of that is automatic. Can be a chemical structure file, used to continue working in different applications, but it can also be office documents you can project or share in the email. Reports can also be database locations, some companies have strict policies on record keeping...

Because the use cases we're exploring with regards to education are very transient, we've chosen to hide the ability to create reports. This helps with explaining and having to consume less when people first see the tool. But this is all just an option away to turn back, so it's really quite easy to do, once we know what it would be used for.

One further note: "exporting" a "file" may not be necessary, when you can just send a URL/link to people you want to share things with. To use an analogy, you don't download youtube videos and email them as attachments :)

In figure 1 you show data that is being pulled from Reaxys. If this was in Marvin Live, and the properties tab was active, the collaborators would have the option to bring in data from databases they have a subscription to, right? Now my question is, what would happen if I was working with someone from a different school, and only one of us had a subscription. Would we both get the data? None of us? Or would we see different things? Are we able to associate different data bases with the molecule we are editing? I guess my question is, Is that data in the property field shared? Or can we each seek different data from different databases while working on a common molecule?
Cheers,
Bob

Hi Bob,
The data coming from the plugins are shared with all participants in a meeting, everyone can see exactly the same. This doesn't only apply for database checks, but also for calculated or predicted properties of the molecules, or other models that are applied in the plugins. Marvin Live in this sense doesn't handle access rights of the meeting participants. The major idea in Marvin Live is to show people the same information to support the discussion as much as possible. In commercial use limiting users to access only a subset of the available data can be solved by authorizing them for pre-defined domains where only selected plugins (i.e. data and feedback access) are active, but within a given meeting people will still be seeing the same.
Cheers,
Ivan

Thank you Andras and Ivan for sharing this interesting project with us.
I'm intrigued by your approach to online office hours. I have tried hosting online office hours with multiple different technology tools (Big Blue Button on Moodle, FUZE, and maybe others that I don't remember). They were clunky. Using MarvinLive looks so much more promising, particularly for organic. Being able to test it out with the sandbox is great. But to know if something will be truly useful I would also need to test it with my students. I cannot tell if that's consistent with your intent for the example you have set up. If it's not, would you be willing to set up a sandbox trial for me to use with students during an online review session?
Regards,
Jennifer

You should by all means test with students. If you look at the video ( https://www.youtube.com/watch?v=PdDWRhvLVQg ), it shows a few use cases we thought about specifically regarding teachers and students. I'd like to hear what you had in mind and if possible, how these ideas work in real life for you.